taxonomy taxonomy2tree $input 0 /dev/null $out_file1 0 taxonomy2tree

**What it does** Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks. ------ **Example** Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation:: 9916 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n 9606 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n Running this tool will generate the following output:: Rank Rank Name Count ------------------------------------- root root 2 superkingdom Eukaryota 2 kingdom Metazoa 2 phylum Chordata 2 subphylum Craniata 2 superclass Gnathostomata 2 class Mammalia 2 superorder Euarchontoglires 1 superorder Laurasiatheria 1 order Primates 1 suborder Haplorrhini 1 suborder Ruminantia 1 superfamily Hominoidea 1 family Bovidae 1 family Hominidae 1 subfamily Bovinae 1 genus Bos 1 genus Homo 1 species Bos taurus 1 species Homo sapiens 1 The output is sorted on Rank and then on Rank Name. .. class:: warningmark **Note** that this tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not.